CN116790823B - Dual quantitative RT-PCR detection composition, kit and method for synchronously detecting HTLV-1 and HTLV-2 - Google Patents

Abstract

The application relates to the field of virus detection, and discloses a nucleic acid composition for synchronously detecting double quantitative RT-PCR of HTLV-1 and HTLV-2, a double quantitative RT-PCR kit for synchronously detecting HTLV-1 and HTLV-2 and a detection method, which are used for solving the problems of uncertain detection results, missed detection and the like of detection methods of HTLV-1 and HTLV-2 two types of human T cell leukemia viruses in the prior art. The application establishes a method for synchronously detecting HTLV-1 and HTLV-2, which has the advantages of high sensitivity, good specificity, repeatability, low reagent cost, convenient use, simple operation and reliable detection result, and strives for precious time for diagnosis and treatment of patients.

Description

Dual quantitative RT-PCR detection composition, kit and method for synchronously detecting HTLV-1 and HTLV-2

Technical Field

The application relates to the field of virus detection, in particular to a nucleic acid composition, a kit and a method for synchronously detecting double quantitative RT-PCR of HTLV-1 and HTLV-2.

Background

Human T cell leukemia virus (human T-cell lymphotropic virus, human T-cell leukemia virus, HTLV) is a single positive strand RNA virus belonging to the retrovirus family. HTLV epidemics are widely distributed worldwide, with major modes of transmission including maternal and infant transmission, sexually transmitted and menstrual transmission. HTLV has 4 subtypes, HTLV-1 and HTLV-2 are two main subtypes, and HTLV can cause various diseases after infection of human body, including adult T lymphocyte leukemia (adult T-cell leukemia, ATL), HTLV-1-related myelopathy/tropical spastic paralysis (HTLV-1 associated myelopathy/tropical spastic paraparesis, HAM/TSP), inflammatory diseases (especially uveitis, arthritis and dermatitis), and immunodeficiency-related diseases (such as T cell immunodeficiency, bronchiectasis, etc.) ^[1] . These diseases have limited treatment means, poor curative effect, poor prognosis of the disease and serious influence on the life quality of patients.

Current HTLV laboratory diagnostics mostly employ Western Blotting (WB) as a confirmation experiment, but in some cases ambiguous results may occur. In addition, conventional antibody detection reagents have difficulty detecting HTLV antibodies when the host is immunodeficient. Therefore, serological detection methods have certain limitations, which can result in missed detection of a portion of HTLV infected individuals. With the popularity of nucleic acid detection techniques, PCR detection is often used as a supplemental test for uncertain samples. However, the prior art does not have a detection method which is efficient, sensitive, low in cost, convenient to use and reliable in detection result for HTLV-1 and HTLV-2.

Disclosure of Invention

In order to overcome the problems, the application aims to establish a high-sensitivity dual quantitative RT-PCR detection method by designing two groups of specific primer probes for HTLV-1 and HTLV-2 gene regions so as to detect HTLV-1 and HTLV-2 virus infection simultaneously, thereby providing technical support for monitoring HTLV-1 and/or HTLV-2 virus load of blood donors and clinical patients in China. The nucleic acid composition, the kit and the detection method for detecting the HTLV-1 and/or the HTLV-2 have the advantages of high sensitivity, good specificity, repeatability, low reagent cost, convenience in use, simplicity in operation and reliable detection result, and precious time is striven for diagnosis and treatment of patients.

In order to achieve the above purpose, the present application adopts the following technical scheme:

1. a set of nucleic acid compositions for dual quantitative RT-PCR for simultaneous detection of HTLV-1 and HTLV-2, characterized in that said nucleic acid compositions comprise an HTLV-1 primer pair, an HTLV-2 primer pair, an HTLV-1 probe and an HTLV-2 probe;

the HTLV-1 primer pair comprises an HTLV-1 forward primer and an HTLV-1 reverse primer, the nucleotide sequence of the HTLV-1 forward primer is shown as SEQ ID NO. 1, and the nucleotide sequence of the HTLV-1 reverse primer is shown as SEQ ID NO. 2;

the HTLV-2 primer pair comprises an HTLV-2 forward primer and an HTLV-2 reverse primer, the nucleotide sequence of the HTLV-2 forward primer is shown as SEQ ID NO. 4, and the nucleotide sequence of the HTLV-2 reverse primer is shown as SEQ ID NO. 5;

the nucleotide sequence of the HTLV-1 probe is shown as SEQ ID NO. 3, and the nucleotide sequence of the HTLV-2 probe is shown as SEQ ID NO. 6.

2. A dual quantitative RT-PCR kit comprising the nucleic acid composition of claim 1 for simultaneous detection of HTLV-1 and HTLV-2.

3. The dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to item 2, wherein the kit further comprises a 2X RT-PCR reagent, taq enzyme, reverse transcriptase, positive control and DNase and RNase free water.

4. A dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to item 2 or 3, characterized in that the concentration of the primer is 20. Mu.M, respectively.

5. A dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to item 4, characterized in that the concentration of the primers is 10. Mu.M, respectively.

6. A dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to item 2 or 3, characterized in that the probe concentrations are 10. Mu.M, respectively.

7. A dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to item 6, characterized in that the probe concentrations are 5. Mu.M, respectively.

8. A dual quantitative RT-PCR kit for quantitatively and synchronously detecting HTLV-1 and HTLV-2 according to item 3, wherein the positive control is a plasmid containing a polynucleotide sequence as shown in SEQ ID NO. 9.

9. A method for simultaneous detection of HTLV-1 and HTLV-2 by using the kit as described in item 2, comprising the steps of:

A. extracting RNA of a sample to be detected;

B. carrying out reverse transcription and fluorescence PCR amplification reaction on RNA of a sample to be detected by using a reagent in the kit;

C. setting a positive control and a negative control, and respectively performing fluorescent PCR amplification reaction on the positive control and the negative control;

D. setting and adjusting a base line and a threshold value according to the signal-to-noise condition, and collecting a fluorescence curve form and a Ct value judgment result of the sample RNA to be detected.

10. The method for simultaneous detection of HTLV-1 and HTLV-2 in accordance with item 9, wherein in step B, the reaction parameters of fluorescent PCR are 42℃for 5min;95 ℃ for 10s,1 cycle; 95℃for 5s,60℃for 34s,40 cycles.

Therefore, the application has the following beneficial effects: (1) The method for synchronously detecting the HTLV-1 and the HTLV-2 is established, the detection speed is high, precious time is striven for diagnosis and treatment of patients, time and labor are saved when two viruses are detected at one time, and the reagent cost is low; (2) The detection method has high sensitivity, good specificity and repeatability, and can effectively eliminate the interference of other viruses; (3) The kit is convenient to use, simple to operate and reliable in detection result.

Drawings

FIG. 1 shows the results of a two-channel assay of HTLV1 primer+probe (HTLV 1-P, FAM label) and HTLV2 primer+probe (HTLV 2-P2, HEX label). The results show that the baseline of each target is uneven, meaning that there is interference between the two probes (HTLV 1-P and HTLV 2-P2).

FIG. 2 is a graph showing the results of detection of the reactivity of two sets of primers and probes with good effect on HTLV1 and HTLV 2. Wherein the 5 'end of the HTLV1-P probe is marked with a FAM fluorescent reporter group, and the 5' end of the HTLV2-P2 probe is marked with a ROX fluorescent reporter group.

FIG. 3 shows the detection reaction of residual plasmid DNA in pseudoviruses. Detecting by using a primer on a pseudovirus mature protein fragment on an expression vector by adopting a SYBR Green I method; the amplification primers adopted are M-F and M-R; the pseudovirus expression vector plasmid DNA is used as a standard substance. Amplification curve, from left to right: (1), (2), (3) and (4) corresponding to the sample templates in sequence: pseudoviral RNA (gDNA Eraser+, RT+), residual plasmid DNA in pseudoviruses (gDNA Eraser-, RT-), pSE380-HTLV1+HTLV2 plasmid, water.

FIG. 4 is a pseudo-viral primary droplet size assay reaction. Detecting by adopting a SYBR Green I method; the amplification primers used were M-F and M-R. The amplified template is cDNA obtained by reverse transcription of the constructed plasmid standard pSE380_STD (diluted in a gradient) and pseudovirus stock RNA. The gradients and the pseudovirus stock samples of the standard are respectively arranged in two parallel. Amplification curve, from left to right: red (1), yellow (2), violet (3), light green (4), green (5), blue (6), corresponding in turn to pseudovirus titres 1 x10 ⁷ Copy/. Mu.l, 1X 10 ⁶ Copy/. Mu.l, pseudovirus stock, 1X 10 ⁵ Copy/. Mu.l, 1X 10 ⁴ Copy/. Mu.l, 1X 10 ³ Copy/. Mu.l.

FIG. 5 shows the detection results of FAM channel corresponding to HTLV1 in a double amplification system. Amplification curve, left to right: red (1), green (2), blue (3) and violet (4) correspond to the virus titres 100000, 10000, 1000 and 100 copies/ul in sequence.

FIG. 6 shows the detection results of the ROX channel corresponding to HTLV2 in the double amplification system. Amplification curve, left to right: yellow (1), green (2), blue (3) and powder (4) correspond to the virus titer of 100000, 10000, 1000 and 100 copies/ul in sequence.

Detailed Description

The present application will be described in further detail with reference to examples and drawings, but embodiments of the present application are not limited thereto.

Explanation of some concepts:

baseline: the baseline of a real-time PCR reaction refers to the signal level during the initial cycle of PCR, typically between 3 and 15 cycles, when there is little change in the fluorescent signal. The low signal may be considered a background or reactive "noise" at this time. The baseline should be set to account for the absence of significant non-background amplified signal while eliminating background in the early amplification cycles. When comparing different qPCR reactions or experiments, the same baseline should be defined.

Threshold value: the threshold value of qPCR represents the level of amplified signal significantly above baseline to distinguish between a well-defined amplified signal and background. Typically, qPCR instruments will have their own software automatically set the threshold to 10 times the standard deviation of the baseline fluorescence value.

Ct: ct refers to the number of cycles corresponding to when the fluorescence signal exceeds the threshold. The Ct value is inversely proportional to the initial amount of the gene of interest and can be used to calculate the initial copy number of DNA. As the amount of template decreases, the number of cycles at which significant amplification is detected increases.

The nucleic acid sequences designed in the present application are shown in Table 1

Table 1: nucleic acid sequences designed in the present application

In Table 1, "-F" represents a forward primer, "-R" represents a reverse primer, and "-P" represents a probe. Wherein "M-F" represents a forward primer of a pseudoviral mature protein used in SYBR Green dye-based quantitative PCR, and "M-R" represents a reverse primer of a pseudoviral mature protein used in SYBR Green dye-based quantitative PCR.

In the application, the 5' end of the probe aiming at HTLV1 or HTLV2 is provided with a fluorescence reporter group, and the fluorescence reporter group can be selected from FAM, ROX, VIC, cy5 or HEX; the 3' end of the fluorescent quenching compound is provided with a fluorescent quenching group, and the fluorescent quenching group can be selected from BHQ1, BHQ2, BHQ3 or MGB. Preferably, the 5 'end of the HTLV1 probe is marked with a FAM fluorescence report group, and the 3' end of the HTLV1 probe is marked with an MGB fluorescence quenching group; preferably, the 5 'end of the HTLV2 probe is marked with a ROX fluorescence report group, and the 3' end of the HTLV2 probe is marked with a BHQ fluorescence quenching group; more preferably, the 5 'end of the HTLV1 probe is marked with a FAM fluorescent reporter group, the 3' end of the HTLV1 probe is marked with an MGB fluorescent quenching group, the 5 'end of the HTLV2 probe is marked with an ROX fluorescent reporter group, and the 3' end of the HTLV2 probe is marked with a BHQ fluorescent quenching group.

Examples

Example 1: construction of plasmid for pSE380-HTLV1+HTLV2 Standard

1.1 Synthesis of genes to obtain pSE380-HTLV1 plasmid

The sequence of the synthesized HTLV1 gene fragment is shown in SEQ ID NO. 7:

SEQ ID NO:7 CTGCAGAAATTAATACGACTCACTATAGGGAGAATTGGCGCAGTATGCTGCCCAGAACAGACGAGGCCTTGATCTCCTGTTCTGGGAGCAAGGAGGATTATGCAAAGCATTACAAGAACAGTGCCGTTTTCCGAAGCTT

the sequence of the synthesized HTLV1 gene fragment is inserted between PstI/HindIII sites of pSE380 plasmid through restriction enzyme digestion and ligase ligation to obtain pSE380-HTLV1 plasmid.

1.2 Synthesizing HTLV2 gene to obtain pSE380-HTLV1+HTLV2 standard quality granules

The sequence of the synthesized HTLV2 gene fragment is shown in SEQ ID NO. 8:

SEQ ID NO:8

GTGCCGTTTTCCGAAGCTAGCCTTCTCTTCGAGGTTGACAAAGATATCTCCCACCTTACCCAGGCCATAGTCAAAAATCATCAAAACATCCTCCGGGTTGCAAGCTTGGCTGTTTTGGC

the above synthesized HTLV2 gene fragment was inserted between Hind III sites of pSE380-HTLV1 plasmid by restriction enzyme digestion and ligase ligation to obtain pSE380-HTLV1+HTLV2 standard plasmid. The sequence of the fragment inserted into the pSE380-HTLV1+HTLV2 standard plasmid is shown in SEQ ID NO. 9:

SEQ ID NO:9

CTGCAGAAATTAATACGACTCACTATAGGGAGAATTGGCGCAGTATGCTGCCCAGAACAGACGAGGCCTTGATCTCCTGTTCTGGGAGCAAGGAGGATTATGCAAAGCATTACAAGAACAGTGCCGTTTTCCGAAGCTAGCCTTCTCTTCGAGGTTGACAAAGATATCTCCCACCTTACCCAGGCCATAGTCAAAAATCATCAAAACATCCTCCGGGTTGCAAGCTT

1.3 Preparation of DH 5. Alpha. Transformed strain containing pSE380-HTLV1+HTLV2 plasmid

DH 5. Alpha. Strain was transformed with pSE380-HTLV1+HTLV2 plasmid, the transformation solution was spread on LB Amp resistance plate, and cultured at 37℃for more than 16 hours to obtain plasmid-containing strain. Several single colonies were picked, glycerol bacteria were prepared and stored at-80 ℃.

1.4 Sequencing the bacterial liquid of the recombinant plasmid to verify the correctness of the inserted sequence.

Example 2: synthesis and reactivity detection of HTLV-1 and HTLV-2 dual detection primer probes

2.1 Synthesis of primer probes

The sequences of HTLV1 and HTLV2 genes and pSE380 plasmid vectors are compared and analyzed, a primer design tool (http:// primrexplore. Jp/e /) is used for designing and synthesizing several groups of primers, blast pair primer pair comparison analysis is used, and after experimental verification, a primer pair with higher species specificity and capable of effectively distinguishing amplified products is finally selected: the sequences of the HTLV1 primer pair and the HTLV2 primer pair are respectively shown as SEQ ID NO. 1-2 and SEQ ID NO. 4-5; in addition, in order to determine the titer of the pseudovirus, a primer pair for amplifying the pseudovirus mature protein fragment on the expression vector is designed, wherein the primer pair is M-F and M-R respectively, and the nucleotide sequences of the primer pair are shown as SEQ ID NO. 10 and 11 respectively. Three probes are respectively designed between the upstream and downstream of the selected primer according to the design principle of the probes, and the sequences of the probes are respectively shown as SEQ ID NO. 3, SEQ ID NO. 6 and SEQ ID NO. 12. The specific sequences of the primers and probes used in the present application are shown in Table 1.

The primers and probes of the application were synthesized by Shanghai Yingjun company. Diluted to 10. Mu. Mol/L with RNase-free water and stored at-20 ℃.

2.2 And the primer probe reaction performance detection uses pSE380+ standard plasmid as a template, a primer pair and a probe are respectively added, and the dual reaction performance of HTLV-1 and HTLV-2 primers and probes is verified. Wherein the plasmid templates used had particle concentrations of 10, respectively ⁶ 、10 ⁵ 、10 ⁴ 、10 ³ 、10 ² Copying/μl;2 μl/system. The amplification primers used are shown in SEQ ID NOS 1-2 and SEQ ID NOS 4-5, respectively, in Table 1,the detection probes used are shown in SEQ ID NOS 3 and 12, respectively, in Table 1. The PCR reaction system was prepared using the reagent Premix Ex Taq (ProbeqPCR) (Takara Code RR 390) as shown in Table 2:

TABLE 2

。

The PCR amplification procedure was: 95 ℃ for 30 seconds; 95 ℃, 5 seconds, 60 ℃,34 seconds, 40 cycles.

In FIG. 1, the fourth is 2X1000 copies of pSE380 standard plasmid, respectively. Wherein the set of curves numbered "(1), (2), (3), (4), (5)" are the results of HTLV1 amplification labeled with FAM; a set of curves numbered "1, 2, 3, 4, 5" are HTLV2 amplification results labeled with HEX.

As can be seen from the experimental results in FIG. 1, the baseline of each target was uneven when HTLV1 and HTLV2 were simultaneously detected using FAM (HTLV 1-P)/HEX (HTLV 2-P2) dual probe mixing. Judging: the two probes interfere with each other.

The probe for HTLV2 was then redesigned to give HTLV2-P1, the sequence of which is shown in SEQ ID NO. 6 of Table 1, and the 5' end of which was fluorescently labeled with ROX. pSE380-HTLV1+HTLV2 standard plasmid was diluted to 1000 copies/. Mu.l as a template, a primer pair and a Probe were added, and the performance of the primer Probe was detected by double mixing, and the PCR reaction system was prepared as shown in Table 3 using the same reagent Premix Ex Taq (Probe qPCR) (Takara Code RR 390):

TABLE 3 Table 3

。

The PCR amplification procedure was: 95 ℃ for 30 seconds; 95 ℃, 5 seconds, 60 ℃,34 seconds, 40 cycles. The results of the double mixing test according to the reaction system of Table 3 are shown in FIG. 2.

The results in FIG. 2 show that the amplification curves of the two primer probes in Table 3 are smooth, the detected Ct values are acceptable, the two labeled amplification curves are not overlapped, and the reaction performance is good and can be used.

Example 3: packaging pSE380-HTLV1+HTLV2 plasmid to obtain MS2 phage pseudovirus, and preparing pseudovirus particles

The strain streaks LB Amp resistance plates to obtain single colonies, the single colonies are selected to be cultured in LB liquid medium, and the single colonies are induced to be cultured by IPTG in logarithmic growth phase, so that pseudo virus particles are expressed.

And (3) performing centrifugal collection on bacterial liquid after induction culture, and then recovering and purifying pseudovirus particles to obtain relatively pure pseudoviruses.

Example 4: extraction of pseudovirion RNA and quantitative detection of titer and purity of pseudovirion

4.1 Extraction of pseudovirion RNA

The stock solution of pseudoviral particles was diluted 100-fold, 5. Mu.l was taken, the volume was made up to 200. Mu.l with DNase-free RNase-free water, and pseudoviral RNA was extracted using the takara virus extraction kit TaKaRa MiniBEST Viral RNA/DNA Extraction Kit Ver.5.0, to obtain a pseudoviral RNA volume of 50. Mu.l.

4.2 Pseudo-virus particle quantitative detection system

Quantification of pseudovirions, detection using SYBR Green I method using primers on the pseudoviral mature protein fragment on the expression vector; the pseudovirus expression vector plasmid DNA is used as a standard substance.

4.2.1 Designing a pair of SYBR Green dye quantitative PCR primers

The sequences are shown as SEQ ID NO 10 and SEQ ID NO 11:

SEQ ID NO:10：M-F：TGTCGACTGGCTCCTACCTGTA

SEQ ID NO:11：M-R：CGTCAACGCTTATGATGGACTCAC

4.2.2 2 μl of pseudoviral RNA was used for reverse transcription and quantitative PCR detection, the reaction system was as follows:

(1) gDNA removal reaction (Takara Code RR 047) in RNA sample, the reaction system is shown in Table 4.

TABLE 4 Table 4

。

The reaction was carried out at 42℃for 2 minutes.

Description: during the DNA residue detection reaction, gDNA is not removed, namely gDNAEras is not added, and water is used for replacing; the RT reaction was also omitted, i.e. PrimeScript RT Enzyme Mix I was omitted and replaced with water. (2) RT reaction (Takara Code RR 047), the reaction system is shown in Table 5.

TABLE 5

。

The reaction system in Table 5 was reacted at 42℃for 15min and then at 95℃for 5 seconds.

(3) PCR (Takara Code RR 820) and the reaction system is shown in Table 6.

TABLE 6

。

The PCR amplification procedure was: 95 ℃ for 30 seconds; 95 ℃, 5 seconds, 60 ℃,34 seconds, 40 cycles.

4.3 Quantitative determination of titre and purity of pseudovirions

4.3.1 Titer detection of pseudovirions and detection of residual plasmid DNA in pseudoviruses

The detection reaction of pseudovirus RNA, (2) the detection reaction of residual plasmid DNA in pseudovirus, (3) the detection reaction of control plasmid, and (4) the negative control reaction are carried out separately. Detecting residual plasmid DNA, and adding pseudovirus RNA which is not treated by gDNA Eraser and is not subjected to reverse transcription reaction as a template; DNA control reaction (i.e., positive control), pSE380-HTLV1+HTLV2 plasmid (1000 copies/. Mu.l) was added as template; adding water as a template in the negative reaction; each reaction was duplicated in parallel. The specific reaction system is shown in Table 7:

TABLE 7

Note that: gEraser is a reagent for removing DNA residues in Takara reagent RR 047; please refer to the specification for details. The system without gEraser and reverse transcriptase is considered to detect contamination mainly with residual DNA.

After the template sample is processed, preparing a PCR reaction according to a PCR reaction system shown in a table 6, and processing an amplified template by a method shown in a table 7; the PCR amplification procedure was: 95 ℃ for 30 seconds; 95 ℃, 5 seconds, 60 ℃,34 seconds, 40 cycles.

The amplification results are shown in FIG. 3. The amplification results show that:

(1) No. reaction (red amplification curve): the template is DNA obtained by the gDNA Eraser+ treatment of the extracted pseudoviral RNA and the reverse transcription reaction; ct is about 12;

(2) The number reaction (blue amplification curve) is a detection reaction of residual plasmid DNA in the pseudovirus, and the template is pseudovirus RNA directly extracted; ct is about 26;

(3) No. (purple amplification curve) for control plasmid detection reaction, template for pSE380-HTLV1+HTLV2 plasmid (1000 copies/. Mu.l); ct value about 26.5;

(4) No. reaction (pink amplification curve), negative control, water without DNase and RNase as template; no amplification.

The Ct difference between reaction 1 and reaction 2 was about 14 cycles, indicating that plasmid DNA remained in the pseudovirus at about 1/10000.

If the Ct difference between the reaction 1 and the reaction 3 is about 14.5 circles, the copy number of the template of the reaction 1 is 10000 times more than that of the reaction 3, and the copy number of the added template DNA of the reaction 3 (in the system) is 2000 copies. From this, the titer of the pseudovirus stock can be approximately calculated. The calculation is as follows:

pseudovirus original droplet size=2000 (copy/2 μl) ×20000 (ct difference about 14.5, template copy number difference greater than 20000 times)

X10 (20. Mu.l cDNA obtained by reverse transcription of 2. Mu.l RNA, 2. Mu.l cDNA was used as PCR template, 10-fold difference)

X10 (5. Mu.l pseudovirus RNA extraction after dilution, 50. Mu.l RNA 10-fold difference)

X100 (100-fold dilution of pseudovirus stock, extraction of rna)

In the quantitative system, the copy number of the pseudovirus is 4x10 ⁷ Copy number/2. Mu.l, 2X10 ⁷ CopyingMu.l; from virus stock to quantification system, 10 is diluted ⁴ Doubling; calculating the titer of pseudovirus stock solution per [ mu ] l to obtain about 2x10 ¹¹ Copy/μl.

4.3.2 Purity quantitative determination result of pseudo virus particle

The pseudovirus purification process is subjected to system optimization, and final detection data show that the DNA pollution level is 1.6 parts per million. Meets the requirements.

Example 5: accurate titre determination of pseudovirions

In order to more accurately determine the titer of the prepared pseudovirus stock on the basis of the preliminary estimated value of pseudovirus titer in example 4, the following accurate titer determination experiment was specially performed.

5.1 Extraction of pseudovirion RNA

Diluting the stock solution of the pseudovirions to 1/10000 by using SM buffer solution; taking 5 μl, and supplementing the volume to 200 μl with DNase-free and RNase-free water; pseudoviral RNA was extracted using the takara virus extraction kit TaKaRa MiniBEST Viral RNA/DNA Extraction Kit Ver.5.0, and the volume of pseudoviral RNA obtained was 50. Mu.l.

5.2 Preparation of standard and accurate quantification of pseudovirion RNA

5.2.1 Standard preparation

Using the constructed plasmid standard pSE380_STD as a template, and carrying out gradient dilution to 10 ⁷ , 10 ⁶ , 10 ⁵ , 10 ⁴ , 10 ³ Copy/. Mu.l.

5.2.2 Accurate quantitative detection system for pseudovirion RNA

Quantification of pseudovirions was detected using the SYBR Green I method using primers on the pseudoviral mature protein fragment on the expression vector.

5.2.2.1 SYBR Green dye method quantitative PCR primer adopting the design

The sequences are shown as SEQ ID NO. 10 and SEQ ID NO. 11.

5.2.2.2 2 μl of pseudoviral RNA was used for reverse transcription and quantitative PCR detection, the reaction system was as follows:

(1) gDNA removal reaction (Takara Code RR 047) in RNA sample, the reaction system is shown in Table 8.

TABLE 8

。

The reaction was carried out at 42℃for 2 minutes.

Note that: in plasmid standard experiments, dH was used ₂ O replaces gDNA Eraser. (2) RT reaction (Takara Code RR 047), the reaction system is shown in Table 9.

TABLE 9

。

The reaction system in Table 9 was reacted at 42℃for 15min and then at 95℃for 5 seconds.

(3) PCR (Takara Code RR 820) and the reaction system is shown in Table 10.

Table 10

。

The PCR amplification procedure was: 95 ℃ for 30 seconds; 95 ℃, 5 seconds, 60 ℃,34 seconds, 40 cycles.

The amplification results are shown in FIG. 4. In FIG. 4, the amplification primers used are M-F and M-R. The amplified template is cDNA obtained by reverse transcription of the constructed plasmid standard pSE380_STD (diluted in a gradient) and pseudovirus stock RNA. The gradients and the pseudovirus stock samples of the standard are respectively arranged in two parallel. Amplification curve, from left to right: red (1), yellow (2), violet (3), light green (4), green (5), blue (6), corresponding in turn to pseudovirus titres 1 x10 ⁷ Copy/. Mu.l, 1X 10 ⁶ Copy/. Mu.l, pseudovirus stock, 1X 10 ⁵ Copy/. Mu.l, 1X 10 ⁴ Copy/. Mu.l, 1X 10 ³ Copy/. Mu.l.

After RNA extraction (5. Mu.l to 50. Mu.l, x 10) and RT-qPCR (2. Mu.l to 20. Mu.l, 10 x) due to virus dilution (x 10000), the virus stock was diluted by 10 ⁶ Doubling; according to the standard curve, the pseudovirus stock virus titer is calculated to be about 2.58 x10 ¹¹ Copy/. Mu.l (average).

Example 6: sensitivity evaluation of HTLV-1/HTLV-2 double quantitative RT-PCR detection method

Pseudovirion stock solution initial titer of 2x10 ¹¹ The pseudovirus titer was diluted to 100000, 10000, 1000, 100, 10 copies/. Mu.l. Pseudoviral RNA was extracted separately and the sensitivity of the HTLV-1/HTLV-2 double quantitative RT-PCR detection method was evaluated. The results are shown in fig. 5 and 6. FIG. 5 shows the detection results of FAM channels corresponding to HTLV1 in a dual amplification system; FIG. 6 shows the detection results of the ROX channel corresponding to HTLV2 in the double amplification system.

The results of fig. 5 and 6 show that the linear relationship between gradients is good. At a pseudovirion concentration of 10 copies/. Mu.l, there is no amplification curve, so the detection sensitivity of the method is in single digit copies.

Example 7: double-probe quantitative PCR reaction system: RR064 (One Step PrimeScriptRT-PCR Kit)

TABLE 11

。

The PCR amplification procedure was: 42 ℃ for 5min;95 ℃ for 10 seconds; 95 ℃, 5 seconds, 60 ℃,34 seconds, 40 cycles.

HTLV is widely distributed worldwide, and the epidemic of HTLV infection in China is mainly concentrated in Fujian, guangdong and Zhejiang 3 provincesThis is related to the greater intimate contact between coastal population and Japanese merchant fishermen +.>. In recent years, the rapid development of Chinese economy brings great population flow at home and abroad, and the epidemic trend of HTLV in China can be changed accordingly.

The nucleic acid detection is used as a supplementary method for an immunology validation experiment, the detection is rapid and accurate, the quantitative detection can be carried out on the viral load, and the nucleic acid detection is very important for the treatment and prognosis of an infected person. Compared with a real-time fluorescence PCR detection system for quantitatively detecting HTLV-1 established in a plurality of laboratories in China, the research successfully designs two groups of probe primers of HTLV-1 and HTLV-2, can perform double quantitative detection on two subtypes of HTLV-1 and HTLV-2, has higher sensitivity, single-digit copy of the sensitivity, good specificity, repeatability, low reagent cost, convenient use, simple operation and reliable detection result, strives for precious time for diagnosis and treatment of patients, and provides technical support for HTLV screening in China.

Reference to the literature

[1] TAGAYA Y, MATSUOKA M, GALLO R. 40 years of the human T-cell leukemia virus: past, present, and future [version 1; peer review: 2 approved][J]. F1000 research, 2019,8: 228.

[2] CAMPOS K R, Gonçalves M G, CATERINO-DE-ARAUJO A. Short Communication: Failures in Detecting HTLV-1 and HTLV-2 in Patients Infected with HIV-1[J]. AIDS Res Hum Retroviruses, 2017, 33(4): 382-385.

[3] Xie Guiyun, chen Jinyan, li Shijie, et al, meta analysis of HTLV infection in continental blood donors in recent 10 years [ J ]. J.China journal of blood transfusion, 2021,34 (12): 1332-1338.

[4] CHEN X, LIU F, FU X, et al. Prevalence of human T-cell lymphotropic virus type-1 infection among blood donors in mainland China: a systematic review and meta-analysis of the last 20 years[J]. Expert Rev Hematol, 2019, 12(8): 579-587。

Claims (10)

1. A set of nucleic acid compositions for dual quantitative RT-PCR for simultaneous detection of HTLV-1 and HTLV-2, characterized in that said nucleic acid compositions are HTLV-1 primer pair, HTLV-2 primer pair, HTLV-1 probe and HTLV-2 probe;

the HTLV-1 primer pair is an HTLV-1 forward primer and an HTLV-1 reverse primer, the nucleotide sequence of the HTLV-1 forward primer is shown as SEQ ID NO. 1, and the nucleotide sequence of the HTLV-1 reverse primer is shown as SEQ ID NO. 2;

the HTLV-2 primer pair is an HTLV-2 forward primer and an HTLV-2 reverse primer, the nucleotide sequence of the HTLV-2 forward primer is shown as SEQ ID NO. 4, and the nucleotide sequence of the HTLV-2 reverse primer is shown as SEQ ID NO. 5;

the nucleotide sequence of the HTLV-1 probe is shown as SEQ ID NO. 3, and the nucleotide sequence of the HTLV-2 probe is shown as SEQ ID NO. 6.

2. A dual quantitative RT-PCR kit comprising the simultaneous detection of HTLV-1 and HTLV-2 of the nucleic acid composition of claim 1.

3. The dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to claim 2, wherein said kit further comprises 2X RT-PCR reagent, taq enzyme, reverse transcriptase, positive control and DNase-free RNase-free water.

4. A dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to claim 2 or 3, wherein the concentration of said primers is 20 μm respectively.

5. The dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to claim 4, wherein the concentration of the primer is 10. Mu.M.

6. A dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to claim 2 or 3, wherein the concentration of said probe is 10 μm respectively.

7. The dual quantitative RT-PCR kit for simultaneous detection of HTLV-1 and HTLV-2 according to claim 6, wherein said probes are each at a concentration of 5 μm.

8. The dual quantitative RT-PCR kit for quantitatively and synchronously detecting HTLV-1 and HTLV-2 according to claim 3, wherein the positive control is a plasmid containing the polynucleotide sequence shown in SEQ ID NO. 9.

9. A method for simultaneous detection of non-diagnostic purposes of HTLV-1 and HTLV-2 double quantitative RT-PCR using the kit of claim 2, comprising the steps of:

A. extracting RNA of a sample to be detected;

B. carrying out reverse transcription and fluorescence PCR amplification reaction on RNA of a sample to be detected by using a reagent in the kit; the reverse transcription and PCR amplification reaction in this step are carried out in one reaction system;

C. setting a positive control and a negative control, and respectively performing fluorescent PCR amplification reaction on the positive control and the negative control;

D. setting and adjusting a base line and a threshold value according to the signal-to-noise condition, and collecting a fluorescence curve form and a Ct value judgment result of the sample RNA to be detected.

10. The method for simultaneous detection of non-diagnostic purposes of HTLV-1 and HTLV-2 double quantitative RT-PCR according to claim 9, wherein in said step B, the reaction parameters of fluorescent PCR are 5min at 42 ℃;95 ℃ for 10s,1 cycle; 95℃for 5s,60℃for 34s,40 cycles.